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how to download the bioimaging data\n\n    source ~/envs/load/bin/activate\n    python load/read_write.py .  # convert data to zarr and save sample\n    deactivate\n\n    source ~/envs/proc/bin/activate\n    python proc/run_3d_segmentation_embryo.py .  # process data\n    deactivate\n\n    cd tgmm/\n    /home/mkcor/tgmm-paper/install/bin/ProcessStack_woGPU config.md 184\n    /home/mkcor/tgmm-paper/install/bin/ProcessStack_woGPU ../data/outputs/sample_frame_184_seg_conn74_rad2.bin 14 14\n    cd ../\n\n    source ~/envs/load/bin/activate\n    python load/save_tgmm_seg.py .  # save result from reproducibility\n    deactivate\n\n    logout\n    scp mkcor@broome.cluster.recurse.com:~/repro-tgmm/data/outputs/*.npz view/.\n    source ~/envs/view/bin/activate\n    cd view/\n    python explore_seg_results.py  # compare segmentation results in napari\n    deactivate\n\n## References\n\nMcDole K, Guignard L, Amat F, Berger A, Malandain G, Royer LA, Turaga SC,\nBranson K, Keller PJ (2018) \"*In Toto* Imaging and Reconstruction of\nPost-Implantation Mouse Development at the Single-Cell Level\" Cell,\n175(3):859-876.e33.\nDOI: [10.1016/j.cell.2018.09.031](http://doi.org/10.1016/j.cell.2018.09.031)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmkcor%2Frepro-tgmm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmkcor%2Frepro-tgmm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmkcor%2Frepro-tgmm/lists"}